The present study investigated the larval fish dispersal along an estuarine–ocean gradient to explore connectivity between ocean and estuaries. During spring 2009, a combined ocean–estuarine survey was conducted along the Lima estuarine salinity gradient and in two transects off the adjacent coast (northwestern Iberian Peninsula), until the 100 m isobaths. Salinity, total particulate matter, particulate organic matter, total dissolved carbon, and dissolved organic carbon reached higher values at the ocean, and chlorophyll a and nutrients increased at the estuary. From the total 56 taxa identified, 14 were present along the gradient, including estuarine species (ES), marine stragglers (MS), and migrants (MM). Canonical correspondence analysis showed that species were separated along the gradient according to their ecological functional classification. MM associated with high salinity were separated from ES correlated with lower salinities and high chlorophyll a concentrations of inner estuary. Flounder (Platichthys flesus) showed a typical spatial gradient of MM, with abundance increasing from the ocean towards inner estuary. The dispersal of larvae along the Lima estuarine–ocean gradient was indicative of connectivity between habitats, emphasizing the need to consider this feature in management plans, mainly for species exploited by commercial fisheries.